Nowadays physicists are confident in their knowledge of nature’s ultimate bits of matter. A handful of building blocks can be easily summarized in a neat little chart.

But merely half a century ago, the situation was messy. During the 1950s, atom smashers produced dozens of previously unknown subatomic particles. Some physicists complained that it would be easier to study botanical nomenclature than learn all the new particle names, most derived from letters in the Greek alphabet. And it seemed strange that nature possessed such a diverse population of particles when only protons, neutrons and electrons sufficed to make all ordinary matter.

But then 50 years ago on February 1, a paper by Murray Gell-Mann appeared in the journal Physics Letters, informing the world about the concept of quarks. It brought order to the subatomic realm.

“We had this list of particles which were all supposedly elementary, and the idea was to find out how they interacted,” Gell-Mann recalled in a 1997 interview. That meant figuring out the nature of the strong nuclear force, the glue that holds protons and neutrons together in the atomic nucleus. Nobody knew why there were so many such strongly interacting particles.

All along, many physicists had believed that the new particles could not all be elementary. Some must have been mashups of more basic components. One popular view, called “nuclear egalitarianism,” held that none of the particles were basic building blocks. Rather they were all made up of various combinations of each other, including themselves.

Pondering these ideas, Gell-Mann constructed tables of particles, sort of like the periodic table of the chemical elements. In 1961 he showed that the particles could be grouped in patterns; gaps in the patterns suggested the existence of undiscovered particles, which did in fact soon show up in experiments, with the properties that Gell-Mann had predicted.

On leave from Caltech in early 1963, Gell-Mann lectured on these issues at MIT. In those talks he noted that the strongly interacting particles could all be formed by combining members of a group of three particles, a triplet. But there was a hitch: those three particles would have electric charges that were fractions of the charge on an electron. No such particle had ever been detected in nature.

A simpler and more elegant scheme can be constructed if we allow non-integral values for the charges. ... We then refer to the members ... of the triplet as ‘quarks.’

“I ignored the fractional charge possibility — it seemed so crazy,” he said.

Then in March 1963, Gell-Mann visited Columbia University in New York, where one day he encountered the physicist Robert Serber at the faculty club. Serber quizzed Gell-Mann about why he didn’t construct the strongly interacting particles from the triplet.

“I said well, I tried it, and I drew on a napkin a picture showing him the equation, showing him the charges would be fractional,” Gell-Mann recalled. “And he said, ‘oh well, I see why.’”

But Serber’s query caused Gell-Mann to reflect more deeply. The next day, he decided that maybe the triplet was the answer after all. It was possible that the particles of the triplet were just always trapped inside the particles they composed and never escaped. That would explain why experiments had never seen particles with fractional charge.

“That was the defining moment, at Columbia, when after Bob Serber asked that question, I thought that well, maybe these things can’t come out and therefore there’s no problem with experiment,” Gell-Mann said.

By the end of 1963, Gell-Mann has written a short paper on the idea and sent it off to Physics Letters, where it was received on January 4, 1964 and published February 1. Titled “A Schematic Model of Baryons and Mesons,” it explained how various combinations of three particles from a triplet could produce baryons (such as protons and neutrons), while two members from the triplet could combine to form a meson (the most famous example at the time being the pi meson, or pion). Maintaining standard electric charges required a fourth particle for this approach to work, Gell-Mann noted in his paper. But “a simpler and more elegant scheme can be constructed if we allow non-integral values for the charges,” he wrote. “We then refer to the members … of the triplet as ‘quarks.’”

He didn’t explain the name in the paper except for a footnote citing James Joyce’s Finnegan’s Wake (Page 383 of the Viking Press 1939 edition). Gell-Mann had encountered a line there — “Three quarks for Muster Mark” — in which “quarks” refer to the squawks of a seagull. He liked the word and thought it appropriate since baryons were composed of three particles.

In his paper, he designated the three quarks as u, d and s — later to be known as up, down and strange. Protons and neutrons require only ups and downs (two ups and a down make a proton, two downs and an up make a neutron). Many of the newly discovered particles, with their strange properties, included a strange quark in the mix.

At about the same time, another physicist, George Zweig, had been working on similar ideas. He called his particles “aces.” But his paper was not published at the time, and he later left physics for biology. Zweig had been a student of Gell-Mann’s at Caltech, but he was working at the CERN laboratory in Geneva while Gell-Mann was at MIT. Neither one knew about what the other was doing.

Gell-Mann once related that in the fall of 1963 he attempted to explain his idea to CERN’s director, Vicktor Weisskopf, over the phone. When he mentioned the fractional charge, Weisskopf responded by saying, “Please, Murray, let us be serious; this is an international call.”

At first there was much confusion about whether quarks were real, or merely mathematical conveniences for classifying bigger particles. Gell-Mann said he always thought they really existed, but he contributed to the confusion with the language he used. He thought that quarks were probably trapped inside other particles, and probably therefore could never be observed, so he referred to any that might escape and become observable as “real” quarks. Those trapped inside he called “mathematical” or “fictitious.”

“By that I meant that they would be trapped inside,” Gell-Mann told me. “I should have stated it better.”

Several years went by before the quark idea caught on. Then in the late 1960s, experiments at the Stanford particle accelerator showed that protons contained some sort of more basic particles (called “partons” by Richard Feynman). Eventually it turned out that the partons were indeed the quarks that Gell-Mann had predicted.

In the decades that followed, new particles turned up that could not be built from the up, down and strange quarks, so the family was expanded. Today the quark chart lists three pairs: the up and down, strange and charm, and bottom and top. A fourth pair would presumably be called high and low, but most evidence suggests that no additional sets of quarks can exist.

That’s not the end of the quark story, though. While the simple picture of up and down quarks making neutrons is essentially correct, real life adds some confusing complications.

In quantum physics, as in spy movies, nothing is ever exactly as it seems. Within a proton, for instance, the two up and one down quarks are not alone. Quantum physics allows other quarks (known as “sea quarks”) to pop in and out of existence. Within nucleons (protons or neutrons) some of those sea quarks are the strange (and antistrange) variety. Various properties of nucleons depend on how much strangeness they contain. It’s an important factor, for instance, in experiments trying to detect the mysterious dark matter in the universe. Less strangeness in the nucleon reduces the likelihood of interaction with a dark matter particle, making detection more difficult.

For the last decade or so, determining the strangeness content of the nucleon has been a major emphasis in nuclear research, but the findings have not been consistent. Various reports (such as here, here and here) don’t all agree with previous work. So experts are still struggling to figure out just exactly what protons and neutrons are made of.

The lesson seems to be that no matter how much physicists find out about matter, there is always a little messiness.